The African coelacanth genome provides insights into tetrapod evolution

Chris T. Amemiya (), Jessica Alföldi (), Alison P. Lee, Shaohua Fan, Hervé Philippe, Iain MacCallum, Ingo Braasch, Tereza Manousaki, Igor Schneider, Nicolas Rohner, Chris Organ, Domitille Chalopin, Jeramiah J. Smith, Mark Robinson, Rosemary A. Dorrington, Marco Gerdol, Bronwen Aken, Maria Assunta Biscotti, Marco Barucca, Denis Baurain, Aaron M. Berlin, Gregory L. Blatch, Francesco Buonocore, Thorsten Burmester, Michael S. Campbell, Adriana Canapa, John P. Cannon, Alan Christoffels, Gianluca De Moro, Adrienne L. Edkins, Lin Fan, Anna Maria Fausto, Nathalie Feiner, Mariko Forconi, Junaid Gamieldien, Sante Gnerre, Andreas Gnirke, Jared V. Goldstone, Wilfried Haerty, Mark E. Hahn, Uljana Hesse, Steve Hoffmann, Jeremy Johnson, Sibel I. Karchner, Shigehiro Kuraku, Marcia Lara, Joshua Z. Levin, Gary W. Litman, Evan Mauceli, Tsutomu Miyake, M. Gail Mueller, David R. Nelson, Anne Nitsche, Ettore Olmo, Tatsuya Ota, Alberto Pallavicini, Sumir Panji, Barbara Picone, Chris P. Ponting, Sonja J. Prohaska, Dariusz Przybylski, Nil Ratan Saha, Vydianathan Ravi, Filipe J. Ribeiro, Tatjana Sauka-Spengler, Giuseppe Scapigliati, Stephen M. J. Searle, Ted Sharpe, Oleg Simakov, Peter F. Stadler, John J. Stegeman, Kenta Sumiyama, Diana Tabbaa, Hakim Tafer, Jason Turner-Maier, Peter van Heusden, Simon White, Louise Williams, Mark Yandell, Henner Brinkmann, Jean-Nicolas Volff, Clifford J. Tabin, Neil Shubin, Manfred Schartl, David B. Jaffe, John H. Postlethwait, Byrappa Venkatesh, Federica Di Palma, Eric S. Lander, Axel Meyer () and Kerstin Lindblad-Toh ()
Additional contact information
Chris T. Amemiya: Molecular Genetics Program, Benaroya Research Institute
Jessica Alföldi: Broad Institute of MIT and Harvard
Alison P. Lee: Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
Shaohua Fan: University of Konstanz
Hervé Philippe: Université de Montréal, Centre Robert Cedergren, Montréal H3T 1J4, Canada
Iain MacCallum: Broad Institute of MIT and Harvard
Ingo Braasch: Institute of Neuroscience, University of Oregon
Tereza Manousaki: University of Konstanz
Igor Schneider: Instituto de Ciencias Biologicas, Universidade Federal do Para
Nicolas Rohner: Harvard Medical School
Chris Organ: University of Utah
Domitille Chalopin: Institut de Genomique Fonctionnelle de Lyon, Ecole Normale Superieure de Lyon, Lyon 69007, France
Jeramiah J. Smith: University of Kentucky
Mark Robinson: Molecular Genetics Program, Benaroya Research Institute
Rosemary A. Dorrington: Biomedical Biotechnology Research Unit (BioBRU), Microbiology & Biotechnology, Rhodes University
Marco Gerdol: University of Trieste
Bronwen Aken: Wellcome Trust Sanger Institute
Maria Assunta Biscotti: Polytechnic University of Marche
Marco Barucca: Polytechnic University of Marche
Denis Baurain: University of Liege
Aaron M. Berlin: Broad Institute of MIT and Harvard
Gregory L. Blatch: Biomedical Biotechnology Research Unit (BioBRU), Microbiology & Biotechnology, Rhodes University
Francesco Buonocore: Agro-food and Forest Systems, University of Tuscia
Thorsten Burmester: University of Hamburg
Michael S. Campbell: Eccles Institute of Human Genetics, University of Utah
Adriana Canapa: Polytechnic University of Marche
John P. Cannon: University of South Florida Morsani College of Medicine, Children’s Research Institute
Alan Christoffels: South African National Bioinformatics Institute, University of the Western Cape
Gianluca De Moro: University of Trieste
Adrienne L. Edkins: Biomedical Biotechnology Research Unit (BioBRU), Microbiology & Biotechnology, Rhodes University
Lin Fan: Broad Institute of MIT and Harvard
Anna Maria Fausto: Agro-food and Forest Systems, University of Tuscia
Nathalie Feiner: University of Konstanz
Mariko Forconi: Polytechnic University of Marche
Junaid Gamieldien: South African National Bioinformatics Institute, University of the Western Cape
Sante Gnerre: Broad Institute of MIT and Harvard
Andreas Gnirke: Broad Institute of MIT and Harvard
Jared V. Goldstone: Woods Hole Oceanographic Institution
Wilfried Haerty: MRC Functional Genomics Unit, Oxford University
Mark E. Hahn: Woods Hole Oceanographic Institution
Uljana Hesse: South African National Bioinformatics Institute, University of the Western Cape
Steve Hoffmann: Transcriptome Bioinformatics Group, LIFE Research Center for Civilization Diseases, Universität Leipzig
Jeremy Johnson: Broad Institute of MIT and Harvard
Sibel I. Karchner: Woods Hole Oceanographic Institution
Shigehiro Kuraku: University of Konstanz
Marcia Lara: Broad Institute of MIT and Harvard
Joshua Z. Levin: Broad Institute of MIT and Harvard
Gary W. Litman: University of South Florida Morsani College of Medicine, Children’s Research Institute
Evan Mauceli: Broad Institute of MIT and Harvard
Tsutomu Miyake: Graduate School of Science and Technology, Keio University
M. Gail Mueller: All Children’s Hospital
David R. Nelson: Immunology and Biochemistry, University of Tennessee Health Science Center
Anne Nitsche: Bioinformatics Group, Universität Leipzig
Ettore Olmo: Polytechnic University of Marche
Tatsuya Ota: The Graduate University for Advanced Studies
Alberto Pallavicini: University of Trieste
Sumir Panji: South African National Bioinformatics Institute, University of the Western Cape
Barbara Picone: South African National Bioinformatics Institute, University of the Western Cape
Chris P. Ponting: MRC Functional Genomics Unit, Oxford University
Sonja J. Prohaska: Computational EvoDevo Group, Universität Leipzig
Dariusz Przybylski: Broad Institute of MIT and Harvard
Nil Ratan Saha: Molecular Genetics Program, Benaroya Research Institute
Vydianathan Ravi: Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
Filipe J. Ribeiro: Broad Institute of MIT and Harvard
Tatjana Sauka-Spengler: Weatherall Institute of Molecular Medicine, University of Oxford
Giuseppe Scapigliati: Agro-food and Forest Systems, University of Tuscia
Stephen M. J. Searle: Wellcome Trust Sanger Institute
Ted Sharpe: Broad Institute of MIT and Harvard
Oleg Simakov: University of Konstanz
Peter F. Stadler: Bioinformatics Group, Universität Leipzig
John J. Stegeman: Woods Hole Oceanographic Institution
Kenta Sumiyama: National Institute of Genetics
Diana Tabbaa: Broad Institute of MIT and Harvard
Hakim Tafer: Bioinformatics Group, Universität Leipzig
Jason Turner-Maier: Broad Institute of MIT and Harvard
Peter van Heusden: South African National Bioinformatics Institute, University of the Western Cape
Simon White: Wellcome Trust Sanger Institute
Louise Williams: Broad Institute of MIT and Harvard
Mark Yandell: Eccles Institute of Human Genetics, University of Utah
Henner Brinkmann: Université de Montréal, Centre Robert Cedergren, Montréal H3T 1J4, Canada
Jean-Nicolas Volff: Institut de Genomique Fonctionnelle de Lyon, Ecole Normale Superieure de Lyon, Lyon 69007, France
Clifford J. Tabin: Harvard Medical School
Neil Shubin: University of Chicago
Manfred Schartl: Biocenter, University of Wuerzburg
David B. Jaffe: Broad Institute of MIT and Harvard
John H. Postlethwait: Institute of Neuroscience, University of Oregon
Byrappa Venkatesh: Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
Federica Di Palma: Broad Institute of MIT and Harvard
Eric S. Lander: Broad Institute of MIT and Harvard
Axel Meyer: University of Konstanz
Kerstin Lindblad-Toh: Broad Institute of MIT and Harvard

Nature, 2013, vol. 496, issue 7445, 311-316

Abstract: Abstract The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.

Date: 2013
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DOI: 10.1038/nature12027

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